DE analysis
gn <- as.character(ls_preprocessed$rna_all$Feature[which(ls_preprocessed$rna_all$Feature_gene_name =='MT-CO1')])
DE_res <- DE_analysis(ls_preprocessed,
GeneBased=TRUE,
pDataBased=FALSE,
NewCondition=FALSE,
cond_nm= gn,
reference = 'low',
correct_gender=TRUE,
extremes_only=TRUE)
## Unlist done
## Labeling done
## Filtering done
## factor levels were dropped which had no samples
## Design done
## factor levels were dropped which had no samples
## Warning: Setting row names on a tibble is deprecated.
## vsd symbols done
## using pre-existing size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
## -- replacing outliers and refitting for 1462 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)
## estimating dispersions
## fitting model and testing
## DESeq done
## using 'normal' for LFC shrinkage, the Normal prior from Love et al (2014).
##
## Note that type='apeglm' and type='ashr' have shown to have less bias than type='normal'.
## See ?lfcShrink for more details on shrinkage type, and the DESeq2 vignette.
## Reference: https://doi.org/10.1093/bioinformatics/bty895
## res symbols done
## list done
DE results
heatmap_200(DE_res$res_df, DE_res$vsd_mat_sym, DE_res$meta_data, DE_res$pData_rnaseq)

x <- DE_res$res_df %>%
arrange(desc(abs(log2FoldChange)))
rownames(x) <- make.names(x$symbol, unique = T)
k <- gn
x <- x[-which(x$gene %in%k),]
#head(x, 10)
vp <- volcano_plot(x, gene=NULL, p_title='MT-CO1', pCutoff=0.001, FCcutoff=1.5)

List of genes differentially expressed (-1.5 > fold change > 1.5, pval<0.001)
vp_tb <- vp$data[which(vp$data$Sig == 'FC_P'),]
rownames(vp_tb) <- c(1:nrow(vp_tb))
kable(vp_tb)
| 1.125816e+05 |
2.353824 |
0.2293886 |
10.335919 |
0.0000000 |
0.0000000 |
ENSG00000198938.2 |
MT-CO3 |
FC_P |
MT.CO3 |
2.353824 |
0.0000000 |
| 5.198489e+03 |
2.278406 |
0.2990219 |
7.574505 |
0.0000000 |
0.0000000 |
ENSG00000237973.1 |
hsa-mir-6723 |
FC_P |
hsa.mir.6723 |
2.278406 |
0.0000000 |
| 5.982732e+04 |
2.203564 |
0.2482062 |
8.994964 |
0.0000000 |
0.0000000 |
ENSG00000198899.2 |
MT-ATP6 |
FC_P |
MT.ATP6 |
2.203564 |
0.0000000 |
| 1.103602e+04 |
2.155337 |
0.2645491 |
8.361639 |
0.0000000 |
0.0000000 |
ENSG00000198840.2 |
MT-ND3 |
FC_P |
MT.ND3 |
2.155337 |
0.0000000 |
| 1.247616e+03 |
2.128188 |
0.2472266 |
8.728586 |
0.0000000 |
0.0000000 |
ENSG00000210196.2 |
MT-TP |
FC_P |
MT.TP |
2.128188 |
0.0000000 |
| 8.698578e+04 |
2.062260 |
0.2484595 |
8.388171 |
0.0000000 |
0.0000000 |
ENSG00000198727.2 |
MT-CYB |
FC_P |
MT.CYB |
2.062260 |
0.0000000 |
| 1.433006e+05 |
2.055945 |
0.2486033 |
8.404454 |
0.0000000 |
0.0000000 |
ENSG00000198886.2 |
MT-ND4 |
FC_P |
MT.ND4 |
2.055945 |
0.0000000 |
| 5.681042e+04 |
2.022377 |
0.2784002 |
7.406580 |
0.0000000 |
0.0000000 |
ENSG00000198763.3 |
MT-ND2 |
FC_P |
MT.ND2 |
2.022377 |
0.0000000 |
| 4.403830e+03 |
2.000968 |
0.2721310 |
7.461931 |
0.0000000 |
0.0000000 |
ENSG00000228253.1 |
MT-ATP8 |
FC_P |
MT.ATP8 |
2.000968 |
0.0000000 |
| 2.143278e+04 |
1.988149 |
0.2558639 |
7.863189 |
0.0000000 |
0.0000000 |
ENSG00000212907.2 |
MT-ND4L |
FC_P |
MT.ND4L |
1.988149 |
0.0000000 |
| 7.148785e+04 |
1.968509 |
0.2600615 |
7.621205 |
0.0000000 |
0.0000000 |
ENSG00000198712.1 |
MT-CO2 |
FC_P |
MT.CO2 |
1.968509 |
0.0000000 |
| 6.830339e+03 |
1.936911 |
0.2729481 |
7.157711 |
0.0000000 |
0.0000000 |
ENSG00000248527.1 |
MTATP6P1 |
FC_P |
MTATP6P1 |
1.936911 |
0.0000000 |
| 1.514651e+02 |
1.924556 |
0.3419348 |
5.761648 |
0.0000000 |
0.0000146 |
ENSG00000134827.3 |
TCN1 |
FC_P |
TCN1 |
1.924556 |
0.0000000 |
| 3.312875e+01 |
1.898496 |
0.2765440 |
7.001108 |
0.0000000 |
0.0000000 |
ENSG00000198744.5 |
RP5-857K21.11 |
FC_P |
RP5.857K21.11 |
1.898496 |
0.0000000 |
| 1.968497e+01 |
1.874076 |
0.3133995 |
6.212204 |
0.0000000 |
0.0000010 |
ENSG00000262902.1 |
RP11-750B16.1 |
FC_P |
RP11.750B16.1 |
1.874076 |
0.0000000 |
| 7.322624e+04 |
1.859089 |
0.2487022 |
7.533098 |
0.0000000 |
0.0000000 |
ENSG00000198888.2 |
MT-ND1 |
FC_P |
MT.ND1 |
1.859089 |
0.0000000 |
| 1.059623e+05 |
1.796863 |
0.2323919 |
7.795807 |
0.0000000 |
0.0000000 |
ENSG00000198786.2 |
MT-ND5 |
FC_P |
MT.ND5 |
1.796863 |
0.0000000 |
| 8.927144e+00 |
1.785540 |
0.3370058 |
4.744627 |
0.0000021 |
0.0013212 |
ENSG00000213759.4 |
UGT2B11 |
FC_P |
UGT2B11 |
1.785540 |
0.0000021 |
| 2.125741e+02 |
1.764552 |
0.3231629 |
5.192940 |
0.0000002 |
0.0002547 |
ENSG00000091137.7 |
SLC26A4 |
FC_P |
SLC26A4 |
1.764552 |
0.0000002 |
| 2.170370e+01 |
1.712493 |
0.3402747 |
5.267992 |
0.0000001 |
0.0001833 |
ENSG00000250748.2 |
RP11-230G5.2 |
FC_P |
RP11.230G5.2 |
1.712493 |
0.0000001 |
| 4.747433e+01 |
1.671178 |
0.3050743 |
5.625947 |
0.0000000 |
0.0000292 |
ENSG00000229344.1 |
RP5-857K21.7 |
FC_P |
RP5.857K21.7 |
1.671178 |
0.0000000 |
| 2.090561e+04 |
1.670813 |
0.2476740 |
6.787578 |
0.0000000 |
0.0000000 |
ENSG00000198695.2 |
MT-ND6 |
FC_P |
MT.ND6 |
1.670813 |
0.0000000 |
| 1.624918e+01 |
1.647497 |
0.3433486 |
5.307120 |
0.0000001 |
0.0001542 |
ENSG00000139151.10 |
PLCZ1 |
FC_P |
PLCZ1 |
1.647497 |
0.0000001 |
| 3.527544e+00 |
1.611987 |
0.3450183 |
5.019375 |
0.0000005 |
NA |
ENSG00000255892.1 |
RP11-459D22.2 |
FC_P |
RP11.459D22.2 |
1.611987 |
0.0000005 |
| 6.197128e+00 |
1.599341 |
0.3374953 |
4.618169 |
0.0000039 |
0.0019283 |
ENSG00000225294.1 |
OSTCP2 |
FC_P |
OSTCP2 |
1.599341 |
0.0000039 |
| 9.915782e+01 |
1.595427 |
0.3334509 |
5.185725 |
0.0000002 |
0.0002548 |
ENSG00000139144.5 |
PIK3C2G |
FC_P |
PIK3C2G |
1.595427 |
0.0000002 |
| 3.501089e+01 |
1.533833 |
0.3180315 |
3.300269 |
0.0009659 |
0.0309132 |
ENSG00000147003.5 |
TMEM27 |
FC_P |
TMEM27 |
1.533833 |
0.0009659 |
| 4.345090e+02 |
1.523048 |
0.3399692 |
4.739014 |
0.0000021 |
0.0013212 |
ENSG00000197301.3 |
RP11-366L20.2 |
FC_P |
RP11.366L20.2 |
1.523048 |
0.0000021 |
| 3.706270e+00 |
-1.500648 |
0.3370660 |
-4.036736 |
0.0000542 |
NA |
ENSG00000104938.12 |
CLEC4M |
FC_P |
CLEC4M |
-1.500648 |
0.0000542 |
Pathway enrichment analysis fGSEA
Low MT-CO1 is the reference. When MT-CO1 is high, pathways shown below are up- or down- regulated
fgsea_res <- fgsea_analysis(DE_res)
## `summarise()` ungrouping output (override with `.groups` argument)
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.02% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.02% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.02% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.02% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.02% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.02% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.02% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.02% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.02% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
fgp <- fgsea_plot(fgsea_res$res_hm, pathways_title='Hallmark', condition_name='MT-CO1 low vs high')

kable(fgp)
| HALLMARK_INFLAMMATORY_RESPONSE |
0.0035211 |
0.0100281 |
-0.5166999 |
-2.728497 |
0 |
193 |
down |
| HALLMARK_TNFA_SIGNALING_VIA_NFKB |
0.0036101 |
0.0100281 |
-0.5024724 |
-2.647208 |
0 |
195 |
down |
| HALLMARK_INTERFERON_GAMMA_RESPONSE |
0.0036101 |
0.0100281 |
-0.4971237 |
-2.615423 |
0 |
194 |
down |
| HALLMARK_MYOGENESIS |
0.0035461 |
0.0100281 |
-0.4898842 |
-2.576125 |
0 |
190 |
down |
| HALLMARK_IL6_JAK_STAT3_SIGNALING |
0.0029155 |
0.0100281 |
-0.5502704 |
-2.476286 |
0 |
82 |
down |
| HALLMARK_INTERFERON_ALPHA_RESPONSE |
0.0029762 |
0.0100281 |
-0.5259010 |
-2.439549 |
0 |
93 |
down |
| HALLMARK_ALLOGRAFT_REJECTION |
0.0035461 |
0.0100281 |
-0.4508472 |
-2.364764 |
0 |
187 |
down |
| HALLMARK_APOPTOSIS |
0.0032787 |
0.0100281 |
-0.4370195 |
-2.215322 |
0 |
155 |
down |
| HALLMARK_UV_RESPONSE_UP |
0.0031250 |
0.0100281 |
-0.4358901 |
-2.192390 |
0 |
147 |
down |
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION |
0.0035211 |
0.0100281 |
-0.3777047 |
-1.986254 |
0 |
189 |
down |
| HALLMARK_APICAL_JUNCTION |
0.0035211 |
0.0100281 |
-0.3765949 |
-1.980417 |
0 |
189 |
down |
| HALLMARK_IL2_STAT5_SIGNALING |
0.0035461 |
0.0100281 |
-0.3710633 |
-1.951289 |
0 |
190 |
down |
| HALLMARK_PROTEIN_SECRETION |
0.0015198 |
0.0100281 |
0.4567544 |
1.926923 |
0 |
89 |
up |
| HALLMARK_P53_PATHWAY |
0.0035461 |
0.0100281 |
-0.3652752 |
-1.920851 |
0 |
190 |
down |
| HALLMARK_COMPLEMENT |
0.0035211 |
0.0100281 |
-0.3611703 |
-1.907204 |
0 |
193 |
down |
| HALLMARK_COAGULATION |
0.0031153 |
0.0100281 |
-0.3748569 |
-1.841698 |
0 |
127 |
down |
| HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY |
0.0025641 |
0.0100281 |
-0.4586332 |
-1.801411 |
0 |
46 |
down |
| HALLMARK_XENOBIOTIC_METABOLISM |
0.0035461 |
0.0100281 |
-0.3365890 |
-1.768958 |
0 |
188 |
down |
| HALLMARK_ADIPOGENESIS |
0.0069444 |
0.0156961 |
-0.3218566 |
-1.681588 |
1 |
183 |
down |
| HALLMARK_HYPOXIA |
0.0069444 |
0.0156961 |
-0.3181967 |
-1.656740 |
1 |
180 |
down |
| HALLMARK_MITOTIC_SPINDLE |
0.0072202 |
0.0156961 |
-0.2773518 |
-1.461190 |
1 |
195 |
down |
| HALLMARK_KRAS_SIGNALING_DN |
0.0070922 |
0.0156961 |
-0.2735489 |
-1.416369 |
1 |
179 |
down |
| HALLMARK_HEME_METABOLISM |
0.0070922 |
0.0156961 |
-0.2691462 |
-1.393572 |
1 |
179 |
down |
| HALLMARK_APICAL_SURFACE |
0.0079156 |
0.0164908 |
-0.4383320 |
-1.674993 |
2 |
42 |
down |
| HALLMARK_PI3K_AKT_MTOR_SIGNALING |
0.0084986 |
0.0169972 |
-0.3378296 |
-1.607182 |
2 |
103 |
down |
| HALLMARK_ESTROGEN_RESPONSE_LATE |
0.0105634 |
0.0203142 |
-0.2599879 |
-1.372898 |
2 |
193 |
down |
| HALLMARK_MYC_TARGETS_V2 |
0.0168539 |
0.0312110 |
-0.3992977 |
-1.659281 |
5 |
57 |
down |
| HALLMARK_ANGIOGENESIS |
0.0203046 |
0.0362582 |
-0.4297947 |
-1.582696 |
7 |
35 |
down |
| HALLMARK_G2M_CHECKPOINT |
0.0248227 |
0.0427978 |
-0.2469708 |
-1.295400 |
6 |
187 |
down |
fgp <- fgsea_plot(fgsea_res$res_c1, pathways_title='C1 positional genes', condition_name='MT-CO1 low vs high')

kable(fgp)
| MT |
0.0017065 |
0.0101893 |
0.9033591 |
3.128845 |
0 |
31 |
up |
| chr14q22 |
0.0016026 |
0.0101893 |
0.6781614 |
2.733202 |
0 |
62 |
up |
| chr14q23 |
0.0015873 |
0.0101893 |
0.6359824 |
2.643019 |
0 |
77 |
up |
| chr14q21 |
0.0015748 |
0.0101893 |
0.6835410 |
2.632522 |
0 |
50 |
up |
| chr7p21 |
0.0016502 |
0.0101893 |
0.6988657 |
2.599868 |
0 |
45 |
up |
| chr6q14 |
0.0015873 |
0.0101893 |
0.6602270 |
2.532750 |
0 |
49 |
up |
| chr8q22 |
0.0015528 |
0.0101893 |
0.5695323 |
2.399848 |
0 |
84 |
up |
| chr12p12 |
0.0015848 |
0.0101893 |
0.5709453 |
2.321493 |
0 |
65 |
up |
| chr5q13 |
0.0016026 |
0.0101893 |
0.5612406 |
2.299213 |
0 |
70 |
up |
| chr6q16 |
0.0017065 |
0.0101893 |
0.6631502 |
2.296866 |
0 |
31 |
up |
| chr12q15 |
0.0017212 |
0.0101893 |
0.6511415 |
2.293115 |
0 |
34 |
up |
| chr1q41 |
0.0015873 |
0.0101893 |
0.5960861 |
2.286694 |
0 |
49 |
up |
| chr12p11 |
0.0016502 |
0.0101893 |
0.6203476 |
2.266348 |
0 |
41 |
up |
| chr5q15 |
0.0016287 |
0.0101893 |
0.6227980 |
2.248737 |
0 |
37 |
up |
| chr14q13 |
0.0016529 |
0.0101893 |
0.5958189 |
2.200769 |
0 |
44 |
up |
| chr10q21 |
0.0016051 |
0.0101893 |
0.5444881 |
2.200221 |
0 |
64 |
up |
| chr2q31 |
0.0015221 |
0.0101893 |
0.5062130 |
2.171557 |
0 |
94 |
up |
| chr3q26 |
0.0014556 |
0.0101893 |
0.4923513 |
2.166231 |
0 |
104 |
up |
| chr12q14 |
0.0015924 |
0.0101893 |
0.5480686 |
2.152203 |
0 |
55 |
up |
| chr5q14 |
0.0016026 |
0.0101893 |
0.5189769 |
2.126073 |
0 |
70 |
up |
| chr8q21 |
0.0015106 |
0.0101893 |
0.4948910 |
2.121953 |
0 |
90 |
up |
| chr7p14 |
0.0014903 |
0.0101893 |
0.4830610 |
2.121799 |
0 |
107 |
up |
| chr5q11 |
0.0016502 |
0.0101893 |
0.5692116 |
2.117538 |
0 |
45 |
up |
| chr1p21 |
0.0015748 |
0.0101893 |
0.5476311 |
2.109092 |
0 |
50 |
up |
| chr1q43 |
0.0016807 |
0.0101893 |
0.6011915 |
2.070108 |
0 |
29 |
up |
| chr1p31 |
0.0014347 |
0.0101893 |
0.4573857 |
2.059690 |
0 |
120 |
up |
| chr11q14 |
0.0015723 |
0.0101893 |
0.4908436 |
2.043308 |
0 |
76 |
up |
| chr15q14 |
0.0016584 |
0.0101893 |
0.5701549 |
2.039194 |
0 |
35 |
up |
| chr5q12 |
0.0016207 |
0.0101893 |
0.5575577 |
2.028013 |
0 |
39 |
up |
| chr5q22 |
0.0016474 |
0.0101893 |
0.5551921 |
2.013379 |
0 |
38 |
up |
fgp <- fgsea_plot(fgsea_res$res_c2, pathways_title='C2 curated genes', condition_name='MT-CO1 low vs high')

kable(fgp)
| SHEN_SMARCA2_TARGETS_UP |
0.0012346 |
0.0230991 |
0.6214452 |
3.185662 |
0 |
407 |
up |
| MILI_PSEUDOPODIA_HAPTOTAXIS_UP |
0.0012180 |
0.0230991 |
0.6094541 |
3.151499 |
0 |
469 |
up |
| SENGUPTA_EBNA1_ANTICORRELATED |
0.0034247 |
0.0230991 |
-0.6104509 |
-2.999846 |
0 |
132 |
down |
| QI_PLASMACYTOMA_UP |
0.0037736 |
0.0230991 |
-0.5389177 |
-2.907804 |
0 |
243 |
down |
| TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_HSC_DN |
0.0034483 |
0.0230991 |
-0.5585107 |
-2.875797 |
0 |
177 |
down |
| BASSO_CD40_SIGNALING_UP |
0.0031348 |
0.0230991 |
-0.6003008 |
-2.843502 |
0 |
100 |
down |
| DIRMEIER_LMP1_RESPONSE_EARLY |
0.0028090 |
0.0230991 |
-0.6496554 |
-2.838583 |
0 |
62 |
down |
| NIKOLSKY_BREAST_CANCER_16P13_AMPLICON |
0.0031646 |
0.0230991 |
-0.5964448 |
-2.831300 |
0 |
105 |
down |
| FAELT_B_CLL_WITH_VH3_21_UP |
0.0025907 |
0.0230991 |
-0.6900536 |
-2.775154 |
0 |
41 |
down |
| DIRMEIER_LMP1_RESPONSE_LATE_UP |
0.0025707 |
0.0230991 |
-0.6595436 |
-2.763610 |
0 |
49 |
down |
| HAMAI_APOPTOSIS_VIA_TRAIL_DN |
0.0035088 |
0.0230991 |
-0.5321489 |
-2.754696 |
0 |
184 |
down |
| KIM_ALL_DISORDERS_DURATION_CORR_DN |
0.0034483 |
0.0230991 |
-0.5573907 |
-2.751626 |
0 |
134 |
down |
| MIKKELSEN_ES_LCP_WITH_H3K4ME3 |
0.0033003 |
0.0230991 |
-0.5555379 |
-2.731132 |
0 |
127 |
down |
| BROWNE_INTERFERON_RESPONSIVE_GENES |
0.0028818 |
0.0230991 |
-0.6095979 |
-2.707059 |
0 |
65 |
down |
| HAMAI_APOPTOSIS_VIA_TRAIL_UP |
0.0011848 |
0.0230991 |
0.5114199 |
2.699999 |
0 |
609 |
up |
| NIKOLSKY_BREAST_CANCER_16Q24_AMPLICON |
0.0025974 |
0.0230991 |
-0.6331548 |
-2.680007 |
0 |
51 |
down |
| PARK_TRETINOIN_RESPONSE_AND_PML_RARA_FUSION |
0.0025126 |
0.0230991 |
-0.7060619 |
-2.659373 |
0 |
29 |
down |
| MULLIGHAN_NPM1_MUTATED_SIGNATURE_2_DN |
0.0028736 |
0.0230991 |
-0.5888260 |
-2.651392 |
0 |
69 |
down |
| ALTEMEIER_RESPONSE_TO_LPS_WITH_MECHANICAL_VENTILATION |
0.0032051 |
0.0230991 |
-0.5468294 |
-2.650769 |
0 |
118 |
down |
| REACTOME_IMMUNOREGULATORY_INTERACTIONS_BETWEEN_A_LYMPHOID_AND_A_NON_LYMPHOID_CELL |
0.0035842 |
0.0230991 |
-0.5185094 |
-2.647499 |
0 |
175 |
down |
| ZHANG_BREAST_CANCER_PROGENITORS_UP |
0.0012346 |
0.0230991 |
0.5148286 |
2.639123 |
0 |
407 |
up |
| GABRIELY_MIR21_TARGETS |
0.0013123 |
0.0230991 |
0.5283675 |
2.633530 |
0 |
271 |
up |
| LIN_APC_TARGETS |
0.0029326 |
0.0230991 |
-0.5987343 |
-2.632837 |
0 |
64 |
down |
| KASLER_HDAC7_TARGETS_1_UP |
0.0037736 |
0.0230991 |
-0.5180264 |
-2.617063 |
0 |
168 |
down |
| VILIMAS_NOTCH1_TARGETS_DN |
0.0025381 |
0.0230991 |
-0.7502278 |
-2.615992 |
0 |
22 |
down |
| AMIT_EGF_RESPONSE_480_HELA |
0.0036765 |
0.0230991 |
-0.5199181 |
-2.596965 |
0 |
151 |
down |
| REACTOME_INTERFERON_ALPHA_BETA_SIGNALING |
0.0027624 |
0.0230991 |
-0.5996013 |
-2.590248 |
0 |
58 |
down |
| NIKOLSKY_BREAST_CANCER_8Q12_Q22_AMPLICON |
0.0014245 |
0.0230991 |
0.5807377 |
2.589905 |
0 |
122 |
up |
| VERHAAK_GLIOBLASTOMA_MESENCHYMAL |
0.0037879 |
0.0230991 |
-0.4963387 |
-2.587929 |
0 |
210 |
down |
| FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_UP |
0.0030488 |
0.0230991 |
-0.5622852 |
-2.577966 |
0 |
83 |
down |
fgp <- fgsea_plot(fgsea_res$res_c3, pathways_title='C3 regulatory target genes', condition_name='MT-CO1 low vs high')

kable(fgp)
| MIR607 |
0.0011261 |
0.0071782 |
0.4944853 |
2.679493 |
0 |
906 |
up |
| MIR576_5P |
0.0012755 |
0.0071782 |
0.5301651 |
2.649113 |
0 |
315 |
up |
| MIR4799_5P |
0.0012346 |
0.0071782 |
0.5115993 |
2.611655 |
0 |
374 |
up |
| MIR3646 |
0.0011561 |
0.0071782 |
0.4803730 |
2.580658 |
0 |
797 |
up |
| HJURP_TARGET_GENES |
0.0015723 |
0.0071782 |
0.6682548 |
2.574568 |
0 |
51 |
up |
| MIR7_2_3P |
0.0011751 |
0.0071782 |
0.4867135 |
2.573177 |
0 |
617 |
up |
| MIR1250_3P |
0.0012210 |
0.0071782 |
0.4936121 |
2.565582 |
0 |
464 |
up |
| MIR3606_3P |
0.0012610 |
0.0071782 |
0.5098986 |
2.564927 |
0 |
332 |
up |
| MIR513A_3P_MIR513C_3P |
0.0012392 |
0.0071782 |
0.4995638 |
2.564281 |
0 |
411 |
up |
| MIR6074 |
0.0013263 |
0.0071782 |
0.5216858 |
2.558826 |
0 |
251 |
up |
| MIR541_5P |
0.0014577 |
0.0071782 |
0.5844128 |
2.558138 |
0 |
111 |
up |
| MIR7_1_3P |
0.0011792 |
0.0071782 |
0.4840289 |
2.557208 |
0 |
619 |
up |
| MIR7856_5P |
0.0012392 |
0.0071782 |
0.5002219 |
2.551287 |
0 |
376 |
up |
| MIR3662 |
0.0011351 |
0.0071782 |
0.4710273 |
2.548929 |
0 |
897 |
up |
| MIR8063 |
0.0012422 |
0.0071782 |
0.4993343 |
2.545229 |
0 |
371 |
up |
| MIR302C_5P |
0.0011862 |
0.0071782 |
0.4805012 |
2.526993 |
0 |
540 |
up |
| MIR3671 |
0.0011655 |
0.0071782 |
0.4765459 |
2.519081 |
0 |
596 |
up |
| MIR380_3P |
0.0013587 |
0.0071782 |
0.5223945 |
2.518560 |
0 |
217 |
up |
| MIR186_5P |
0.0011962 |
0.0071782 |
0.4780738 |
2.507776 |
0 |
529 |
up |
| MIR548AE_3P_MIR548AQ_3P |
0.0011628 |
0.0071782 |
0.4683896 |
2.504792 |
0 |
737 |
up |
| MIR3133 |
0.0012285 |
0.0071782 |
0.4810222 |
2.498855 |
0 |
472 |
up |
| MIR548J_3P |
0.0011723 |
0.0071782 |
0.4679042 |
2.498530 |
0 |
734 |
up |
| MIR12124 |
0.0012837 |
0.0071782 |
0.4995472 |
2.484906 |
0 |
303 |
up |
| MIR548AH_3P_MIR548AM_3P |
0.0011710 |
0.0071782 |
0.4650212 |
2.483253 |
0 |
733 |
up |
| MIR548N |
0.0011792 |
0.0071782 |
0.4699310 |
2.473825 |
0 |
568 |
up |
| MIR32_3P |
0.0012788 |
0.0071782 |
0.4960537 |
2.471391 |
0 |
310 |
up |
| MIR3143 |
0.0012361 |
0.0071782 |
0.4776853 |
2.465106 |
0 |
430 |
up |
| MIR34C_3P |
0.0015723 |
0.0071782 |
0.6228463 |
2.461628 |
0 |
62 |
up |
| MIR548AJ_3P_MIR548X_3P |
0.0011325 |
0.0071782 |
0.4528336 |
2.446967 |
0 |
853 |
up |
| MIR4680_3P |
0.0013441 |
0.0071782 |
0.5023971 |
2.443385 |
0 |
239 |
up |
fgp <- fgsea_plot(fgsea_res$res_c4, pathways_title='C4 cancer', condition_name='MT-CO1 low vs high')

kable(fgp)
| GNF2_ITGB2 |
0.0025126 |
0.0156526 |
-0.6911401 |
-2.895633 |
0 |
51 |
down |
| GNF2_TNFRSF1B |
0.0025445 |
0.0156526 |
-0.6519754 |
-2.855359 |
0 |
59 |
down |
| GNF2_S100A4 |
0.0024331 |
0.0156526 |
-0.6957840 |
-2.778754 |
0 |
44 |
down |
| GNF2_FGR |
0.0024390 |
0.0156526 |
-0.7620046 |
-2.769924 |
0 |
30 |
down |
| GNF2_IL2RB |
0.0025381 |
0.0156526 |
-0.7025898 |
-2.684422 |
0 |
37 |
down |
| MODULE_430 |
0.0026178 |
0.0156526 |
-0.6316267 |
-2.682751 |
0 |
54 |
down |
| MODULE_257 |
0.0033223 |
0.0156526 |
-0.5271417 |
-2.669231 |
0 |
150 |
down |
| MODULE_241 |
0.0028249 |
0.0156526 |
-0.5840829 |
-2.636794 |
0 |
70 |
down |
| GNF2_PTPN4 |
0.0024331 |
0.0156526 |
-0.6549595 |
-2.615714 |
0 |
44 |
down |
| MODULE_174 |
0.0030211 |
0.0156526 |
-0.5507038 |
-2.576494 |
0 |
92 |
down |
| GNF2_CASP1 |
0.0030211 |
0.0156526 |
-0.5320882 |
-2.559521 |
0 |
103 |
down |
| GNF2_CD7 |
0.0025000 |
0.0156526 |
-0.6599203 |
-2.504273 |
0 |
36 |
down |
| MODULE_291 |
0.0026954 |
0.0156526 |
-0.5727886 |
-2.500499 |
0 |
62 |
down |
| MODULE_79 |
0.0030030 |
0.0156526 |
-0.5324167 |
-2.499789 |
0 |
95 |
down |
| MODULE_128 |
0.0030030 |
0.0156526 |
-0.5331226 |
-2.496941 |
0 |
93 |
down |
| GNF2_HCK |
0.0031348 |
0.0156526 |
-0.5363299 |
-2.483143 |
0 |
89 |
down |
| GNF2_RAB7L1 |
0.0024390 |
0.0156526 |
-0.6790360 |
-2.468329 |
0 |
30 |
down |
| MODULE_484 |
0.0024213 |
0.0156526 |
-0.6282085 |
-2.468025 |
0 |
41 |
down |
| GNF2_MYD88 |
0.0026042 |
0.0156526 |
-0.5768283 |
-2.467434 |
0 |
55 |
down |
| MODULE_170 |
0.0030030 |
0.0156526 |
-0.5216000 |
-2.449002 |
0 |
95 |
down |
| GNF2_PECAM1 |
0.0025575 |
0.0156526 |
-0.5708076 |
-2.422301 |
0 |
53 |
down |
| MODULE_20 |
0.0029326 |
0.0156526 |
-0.5342236 |
-2.405219 |
0 |
74 |
down |
| GNF2_CYP2B6 |
0.0024752 |
0.0156526 |
-0.5935187 |
-2.400250 |
0 |
46 |
down |
| GNF2_MATK |
0.0023981 |
0.0156526 |
-0.6969473 |
-2.400119 |
0 |
24 |
down |
| MORF_PML |
0.0031546 |
0.0156526 |
-0.4810702 |
-2.388631 |
0 |
131 |
down |
| MORF_ARAF1 |
0.0029499 |
0.0156526 |
-0.5305289 |
-2.379562 |
0 |
73 |
down |
| GNF2_CARD15 |
0.0027548 |
0.0156526 |
-0.5392377 |
-2.377421 |
0 |
65 |
down |
| MORF_GPX4 |
0.0024938 |
0.0156526 |
-0.5697568 |
-2.371449 |
0 |
50 |
down |
| GNF2_HLA_C |
0.0024213 |
0.0156526 |
-0.6034493 |
-2.370755 |
0 |
41 |
down |
| MODULE_350 |
0.0026178 |
0.0156526 |
-0.5465875 |
-2.358469 |
0 |
57 |
down |
fgp <- fgsea_plot(fgsea_res$res_c5, pathways_title='C5 GO genes', condition_name='MT-CO1 low vs high')

kable(fgp)
| GO_ALPHA_BETA_T_CELL_ACTIVATION |
0.0031348 |
0.0414217 |
-0.5193727 |
-2.518853 |
0 |
131 |
down |
| GO_T_CELL_DIFFERENTIATION |
0.0037879 |
0.0414217 |
-0.4683992 |
-2.480167 |
0 |
233 |
down |
| GO_POSITIVE_REGULATION_OF_CELL_ACTIVATION |
0.0046083 |
0.0414217 |
-0.4402180 |
-2.455196 |
0 |
355 |
down |
| GO_NEGATIVE_REGULATION_OF_CYTOKINE_PRODUCTION_INVOLVED_IN_IMMUNE_RESPONSE |
0.0023310 |
0.0414217 |
-0.7119093 |
-2.445444 |
0 |
23 |
down |
| GO_LYMPHOCYTE_DIFFERENTIATION |
0.0043668 |
0.0414217 |
-0.4381459 |
-2.430159 |
0 |
327 |
down |
| GO_T_CELL_RECEPTOR_COMPLEX |
0.0028329 |
0.0414217 |
-0.5344270 |
-2.422824 |
0 |
90 |
down |
| GO_POSITIVE_REGULATION_OF_INTERLEUKIN_4_PRODUCTION |
0.0023148 |
0.0414217 |
-0.7074415 |
-2.409413 |
0 |
22 |
down |
| GO_REGULATION_OF_T_CELL_ACTIVATION |
0.0042017 |
0.0414217 |
-0.4356865 |
-2.392107 |
0 |
303 |
down |
| GO_REGULATION_OF_ANTIGEN_PROCESSING_AND_PRESENTATION |
0.0022936 |
0.0414217 |
-0.7333934 |
-2.391422 |
0 |
19 |
down |
| GO_ALPHA_BETA_T_CELL_DIFFERENTIATION |
0.0029070 |
0.0414217 |
-0.5228599 |
-2.386759 |
0 |
98 |
down |
| GO_REGULATION_OF_INFLAMMATORY_RESPONSE |
0.0043668 |
0.0414217 |
-0.4299698 |
-2.384810 |
0 |
327 |
down |
| GO_LEUKOCYTE_PROLIFERATION |
0.0040323 |
0.0414217 |
-0.4400706 |
-2.378877 |
0 |
275 |
down |
| GO_NEGATIVE_REGULATION_OF_INFLAMMATORY_RESPONSE |
0.0033003 |
0.0414217 |
-0.4894358 |
-2.378345 |
0 |
140 |
down |
| GO_RESPIRASOME |
0.0015314 |
0.0414217 |
0.5564150 |
2.373546 |
0 |
88 |
up |
| GO_NEGATIVE_REGULATION_OF_INTERLEUKIN_6_PRODUCTION |
0.0026385 |
0.0414217 |
-0.5860676 |
-2.372996 |
0 |
49 |
down |
| GO_LEUKOCYTE_CELL_CELL_ADHESION |
0.0045249 |
0.0414217 |
-0.4299917 |
-2.369350 |
0 |
320 |
down |
| GO_STEROID_CATABOLIC_PROCESS |
0.0023866 |
0.0414217 |
-0.6695197 |
-2.367841 |
0 |
25 |
down |
| GO_PROTEIN_LIPID_COMPLEX_BINDING |
0.0025253 |
0.0414217 |
-0.6496216 |
-2.364210 |
0 |
29 |
down |
| GO_REGULATION_OF_IMMUNE_EFFECTOR_PROCESS |
0.0046948 |
0.0414217 |
-0.4163965 |
-2.360824 |
0 |
420 |
down |
| GO_NEGATIVE_REGULATION_OF_DEFENSE_RESPONSE |
0.0035211 |
0.0414217 |
-0.4513739 |
-2.360095 |
0 |
206 |
down |
| GO_POSITIVE_REGULATION_OF_LEUKOCYTE_CELL_CELL_ADHESION |
0.0036630 |
0.0414217 |
-0.4522428 |
-2.357548 |
0 |
209 |
down |
| GO_REGULATION_OF_PRODUCTION_OF_MOLECULAR_MEDIATOR_OF_IMMUNE_RESPONSE |
0.0031348 |
0.0414217 |
-0.4843216 |
-2.348863 |
0 |
131 |
down |
| GO_ATP_SYNTHESIS_COUPLED_ELECTRON_TRANSPORT |
0.0015314 |
0.0414217 |
0.5498380 |
2.345490 |
0 |
88 |
up |
| GO_NADH_DEHYDROGENASE_ACTIVITY |
0.0016556 |
0.0414217 |
0.6345283 |
2.341045 |
0 |
44 |
up |
| GO_POSITIVE_REGULATION_OF_ERK1_AND_ERK2_CASCADE |
0.0034247 |
0.0414217 |
-0.4523257 |
-2.333569 |
0 |
188 |
down |
| GO_RESPONSE_TO_PEPTIDOGLYCAN |
0.0022472 |
0.0414217 |
-0.8702731 |
-2.333207 |
0 |
10 |
down |
| GO_CELLULAR_RESPONSE_TO_BIOTIC_STIMULUS |
0.0037175 |
0.0414217 |
-0.4445874 |
-2.331516 |
0 |
219 |
down |
| GO_REGULATION_OF_NEUTROPHIL_ACTIVATION |
0.0022676 |
0.0414217 |
-0.8414661 |
-2.326205 |
0 |
11 |
down |
| GO_INTEGRIN_MEDIATED_SIGNALING_PATHWAY |
0.0028902 |
0.0414217 |
-0.5085460 |
-2.323330 |
0 |
97 |
down |
| GO_SYNCYTIUM_FORMATION |
0.0026178 |
0.0414217 |
-0.5681441 |
-2.319278 |
0 |
50 |
down |
fgp <- fgsea_plot(fgsea_res$res_c6, pathways_title='C6 oncogenic', condition_name='MT-CO1 low vs high')

kable(fgp)
| PRC2_EED_UP.V1_DN |
0.0033670 |
0.0097609 |
-0.5424789 |
-2.792733 |
0 |
179 |
down |
| CYCLIN_D1_UP.V1_UP |
0.0034014 |
0.0097609 |
-0.5217470 |
-2.660610 |
0 |
173 |
down |
| PIGF_UP.V1_UP |
0.0014124 |
0.0097609 |
0.5215918 |
2.460068 |
0 |
181 |
up |
| PDGF_ERK_DN.V1_DN |
0.0032362 |
0.0097609 |
-0.4943174 |
-2.439401 |
0 |
141 |
down |
| ATF2_UP.V1_UP |
0.0032362 |
0.0097609 |
-0.4745666 |
-2.421739 |
0 |
165 |
down |
| RAPA_EARLY_UP.V1_DN |
0.0033670 |
0.0097609 |
-0.4735251 |
-2.411170 |
0 |
167 |
down |
| IL15_UP.V1_UP |
0.0033898 |
0.0097609 |
-0.4445118 |
-2.269528 |
0 |
174 |
down |
| VEGF_A_UP.V1_UP |
0.0034130 |
0.0097609 |
-0.4387310 |
-2.238506 |
0 |
177 |
down |
| PIGF_UP.V1_DN |
0.0033670 |
0.0097609 |
-0.4338658 |
-2.215623 |
0 |
169 |
down |
| TBK1.DF_DN |
0.0013369 |
0.0097609 |
0.4449224 |
2.212234 |
0 |
265 |
up |
| SRC_UP.V1_UP |
0.0032895 |
0.0097609 |
-0.4438094 |
-2.204890 |
0 |
148 |
down |
| HINATA_NFKB_IMMU_INF |
0.0022676 |
0.0097609 |
-0.7483708 |
-2.163509 |
0 |
14 |
down |
| BMI1_DN_MEL18_DN.V1_UP |
0.0033445 |
0.0097609 |
-0.4386359 |
-2.143131 |
0 |
135 |
down |
| CYCLIN_D1_KE_.V1_UP |
0.0034130 |
0.0097609 |
-0.4154743 |
-2.127258 |
0 |
178 |
down |
| IL2_UP.V1_UP |
0.0033557 |
0.0097609 |
-0.4142684 |
-2.112426 |
0 |
170 |
down |
| MEL18_DN.V1_UP |
0.0032680 |
0.0097609 |
-0.4366196 |
-2.106819 |
0 |
129 |
down |
| RAPA_EARLY_UP.V1_UP |
0.0031949 |
0.0097609 |
-0.4213389 |
-2.095798 |
0 |
146 |
down |
| RB_P107_DN.V1_UP |
0.0033113 |
0.0097609 |
-0.4307204 |
-2.073399 |
0 |
128 |
down |
| GCNP_SHH_UP_LATE.V1_DN |
0.0033670 |
0.0097609 |
-0.4054377 |
-2.064472 |
0 |
167 |
down |
| ERBB2_UP.V1_DN |
0.0014085 |
0.0097609 |
0.4361698 |
2.058619 |
0 |
182 |
up |
| BMI1_DN.V1_UP |
0.0033557 |
0.0097609 |
-0.4226519 |
-2.047233 |
0 |
133 |
down |
| ALK_DN.V1_UP |
0.0033113 |
0.0097609 |
-0.4258265 |
-2.030372 |
0 |
124 |
down |
| CSR_LATE_UP.V1_DN |
0.0033113 |
0.0097609 |
-0.4124100 |
-1.995100 |
0 |
130 |
down |
| ATF2_S_UP.V1_DN |
0.0033557 |
0.0097609 |
-0.3903671 |
-1.994436 |
0 |
172 |
down |
| LEF1_UP.V1_UP |
0.0033670 |
0.0097609 |
-0.3855136 |
-1.984660 |
0 |
179 |
down |
| KRAS.AMP.LUNG_UP.V1_DN |
0.0032258 |
0.0097609 |
-0.4128406 |
-1.970052 |
0 |
120 |
down |
| RB_DN.V1_UP |
0.0033113 |
0.0097609 |
-0.4141831 |
-1.967801 |
0 |
123 |
down |
| ESC_V6.5_UP_EARLY.V1_DN |
0.0033670 |
0.0097609 |
-0.3883519 |
-1.936019 |
0 |
152 |
down |
| SNF5_DN.V1_UP |
0.0033670 |
0.0097609 |
-0.3857501 |
-1.923048 |
0 |
152 |
down |
| RB_P130_DN.V1_UP |
0.0031447 |
0.0097609 |
-0.4024186 |
-1.914111 |
0 |
114 |
down |
fgp <- fgsea_plot(fgsea_res$res_c7, pathways_title='C7 immunologic', condition_name='MT-CO1 low vs high')

kable(fgp)
| GSE369_PRE_VS_POST_IL6_INJECTION_SOCS3_KO_LIVER_DN |
0.0036630 |
0.0089815 |
-0.6451392 |
-3.350586 |
0 |
187 |
down |
| GSE9988_LPS_VS_VEHICLE_TREATED_MONOCYTE_DN |
0.0036232 |
0.0089815 |
-0.6071365 |
-3.172598 |
0 |
191 |
down |
| GSE9988_ANTI_TREM1_AND_LPS_VS_VEHICLE_TREATED_MONOCYTES_DN |
0.0035842 |
0.0089815 |
-0.6003589 |
-3.127074 |
0 |
189 |
down |
| GSE9006_TYPE_1_VS_TYPE_2_DIABETES_PBMC_AT_DX_UP |
0.0036630 |
0.0089815 |
-0.6005153 |
-3.118827 |
0 |
187 |
down |
| GSE9601_UNTREATED_VS_PI3K_INHIBITOR_TREATED_HCMV_INF_MONOCYTE_UP |
0.0036232 |
0.0089815 |
-0.6029732 |
-3.091378 |
0 |
162 |
down |
| GSE9988_ANTI_TREM1_VS_VEHICLE_TREATED_MONOCYTES_DN |
0.0035971 |
0.0089815 |
-0.5900630 |
-3.083918 |
0 |
190 |
down |
| GSE36527_CD69_NEG_VS_POS_TREG_CD62L_LOS_KLRG1_NEG_DN |
0.0035587 |
0.0089815 |
-0.5691509 |
-2.958206 |
0 |
183 |
down |
| GSE6269_HEALTHY_VS_FLU_INF_PBMC_DN |
0.0033898 |
0.0089815 |
-0.5834221 |
-2.956426 |
0 |
148 |
down |
| GSE16385_MONOCYTE_VS_12H_IL4_TREATED_MACROPHAGE_DN |
0.0035587 |
0.0089815 |
-0.5674304 |
-2.949263 |
0 |
183 |
down |
| GSE27670_BLIMP1_VS_LMP1_TRANSDUCED_GC_BCELL_UP |
0.0035587 |
0.0089815 |
-0.5618871 |
-2.920451 |
0 |
183 |
down |
| GSE360_L_DONOVANI_VS_B_MALAYI_HIGH_DOSE_MAC_DN |
0.0035461 |
0.0089815 |
-0.5614279 |
-2.919446 |
0 |
184 |
down |
| GSE10325_LUPUS_BCELL_VS_LUPUS_MYELOID_DN |
0.0034965 |
0.0089815 |
-0.5549483 |
-2.912236 |
0 |
192 |
down |
| GSE360_DC_VS_MAC_B_MALAYI_HIGH_DOSE_DN |
0.0035461 |
0.0089815 |
-0.5595859 |
-2.909867 |
0 |
184 |
down |
| GSE7218_UNSTIM_VS_ANTIGEN_STIM_THROUGH_IGG_BCELL_DN |
0.0035714 |
0.0089815 |
-0.5660759 |
-2.898726 |
0 |
159 |
down |
| GSE22140_HEALTHY_VS_ARTHRITIC_GERMFREE_MOUSE_CD4_TCELL_DN |
0.0036232 |
0.0089815 |
-0.5534128 |
-2.891865 |
0 |
191 |
down |
| GSE9006_HEALTHY_VS_TYPE_2_DIABETES_PBMC_AT_DX_UP |
0.0034965 |
0.0089815 |
-0.5568072 |
-2.891208 |
0 |
181 |
down |
| GSE10325_BCELL_VS_MYELOID_DN |
0.0035587 |
0.0089815 |
-0.5549508 |
-2.884399 |
0 |
183 |
down |
| GSE23568_CTRL_TRANSDUCED_VS_WT_CD8_TCELL_DN |
0.0036101 |
0.0089815 |
-0.5521093 |
-2.872602 |
0 |
188 |
down |
| GSE24634_TREG_VS_TCONV_POST_DAY10_IL4_CONVERSION_DN |
0.0036101 |
0.0089815 |
-0.5485671 |
-2.854171 |
0 |
188 |
down |
| GSE7460_TREG_VS_TCONV_ACT_WITH_TGFB_DN |
0.0035461 |
0.0089815 |
-0.5471283 |
-2.827283 |
0 |
176 |
down |
| GSE10325_LUPUS_CD4_TCELL_VS_LUPUS_MYELOID_DN |
0.0036630 |
0.0089815 |
-0.5431416 |
-2.822144 |
0 |
186 |
down |
| GSE360_HIGH_DOSE_B_MALAYI_VS_M_TUBERCULOSIS_MAC_UP |
0.0036630 |
0.0089815 |
-0.5382570 |
-2.795484 |
0 |
187 |
down |
| GSE5099_UNSTIM_VS_MCSF_TREATED_MONOCYTE_DAY3_DN |
0.0036101 |
0.0089815 |
-0.5368805 |
-2.793366 |
0 |
188 |
down |
| GSE28726_NAIVE_CD4_TCELL_VS_NAIVE_NKTCELL_DN |
0.0036630 |
0.0089815 |
-0.5329758 |
-2.769323 |
0 |
186 |
down |
| GSE9988_LOW_LPS_VS_VEHICLE_TREATED_MONOCYTE_DN |
0.0035971 |
0.0089815 |
-0.5276631 |
-2.757790 |
0 |
190 |
down |
| GSE3337_CTRL_VS_16H_IFNG_IN_CD8POS_DC_DN |
0.0034483 |
0.0089815 |
-0.5296092 |
-2.757252 |
0 |
180 |
down |
| GSE13485_DAY1_VS_DAY21_YF17D_VACCINE_PBMC_DN |
0.0013889 |
0.0089815 |
0.5829842 |
2.748039 |
0 |
176 |
up |
| GSE44649_NAIVE_VS_ACTIVATED_CD8_TCELL_MIR155_KO_DN |
0.0013736 |
0.0089815 |
0.5747852 |
2.726770 |
0 |
185 |
up |
| GSE32986_CURDLAN_HIGHDOSE_VS_GMCSF_AND_CURDLAN_HIGHDOSE_STIM_DC_DN |
0.0034965 |
0.0089815 |
-0.5191115 |
-2.724173 |
0 |
192 |
down |
| GSE9988_ANTI_TREM1_VS_ANTI_TREM1_AND_LPS_MONOCYTE_UP |
0.0035088 |
0.0089815 |
-0.5178045 |
-2.721045 |
0 |
194 |
down |
fgp <- fgsea_plot(fgsea_res$res_msg, pathways_title='All signatures', condition_name='MT-CO1 low vs high')

kable(fgp)
| GSE369_PRE_VS_POST_IL6_INJECTION_SOCS3_KO_LIVER_DN |
0.0034722 |
0.0197796 |
-0.6451392 |
-3.367435 |
0 |
187 |
down |
| SHEN_SMARCA2_TARGETS_UP |
0.0012563 |
0.0197796 |
0.6214452 |
3.217144 |
0 |
407 |
up |
| MILI_PSEUDOPODIA_HAPTOTAXIS_UP |
0.0012255 |
0.0197796 |
0.6094541 |
3.181855 |
0 |
469 |
up |
| GSE9988_LPS_VS_VEHICLE_TREATED_MONOCYTE_DN |
0.0035842 |
0.0197796 |
-0.6071365 |
-3.167430 |
0 |
191 |
down |
| chr16p11 |
0.0031056 |
0.0197796 |
-0.6427102 |
-3.161449 |
0 |
120 |
down |
| GSE9988_ANTI_TREM1_AND_LPS_VS_VEHICLE_TREATED_MONOCYTES_DN |
0.0035211 |
0.0197796 |
-0.6003589 |
-3.138130 |
0 |
189 |
down |
| GSE9006_TYPE_1_VS_TYPE_2_DIABETES_PBMC_AT_DX_UP |
0.0034722 |
0.0197796 |
-0.6005153 |
-3.134511 |
0 |
187 |
down |
| MT |
0.0015949 |
0.0197796 |
0.9033591 |
3.126380 |
0 |
31 |
up |
| chr9q34 |
0.0036101 |
0.0197796 |
-0.5864285 |
-3.095703 |
0 |
210 |
down |
| GSE9988_ANTI_TREM1_VS_VEHICLE_TREATED_MONOCYTES_DN |
0.0035088 |
0.0197796 |
-0.5900630 |
-3.083390 |
0 |
190 |
down |
| GSE9601_UNTREATED_VS_PI3K_INHIBITOR_TREATED_HCMV_INF_MONOCYTE_UP |
0.0035587 |
0.0197796 |
-0.6029732 |
-3.079737 |
0 |
162 |
down |
| SENGUPTA_EBNA1_ANTICORRELATED |
0.0032680 |
0.0197796 |
-0.6104509 |
-3.030616 |
0 |
132 |
down |
| chr22q11 |
0.0036765 |
0.0197796 |
-0.5603387 |
-2.967030 |
0 |
214 |
down |
| GSE6269_HEALTHY_VS_FLU_INF_PBMC_DN |
0.0033113 |
0.0197796 |
-0.5834221 |
-2.963032 |
0 |
148 |
down |
| GSE36527_CD69_NEG_VS_POS_TREG_CD62L_LOS_KLRG1_NEG_DN |
0.0035587 |
0.0197796 |
-0.5691509 |
-2.959361 |
0 |
183 |
down |
| GSE16385_MONOCYTE_VS_12H_IL4_TREATED_MACROPHAGE_DN |
0.0035587 |
0.0197796 |
-0.5674304 |
-2.950415 |
0 |
183 |
down |
| GSE27670_BLIMP1_VS_LMP1_TRANSDUCED_GC_BCELL_UP |
0.0035587 |
0.0197796 |
-0.5618871 |
-2.921592 |
0 |
183 |
down |
| GSE360_L_DONOVANI_VS_B_MALAYI_HIGH_DOSE_MAC_DN |
0.0035714 |
0.0197796 |
-0.5614279 |
-2.916767 |
0 |
184 |
down |
| GSE360_DC_VS_MAC_B_MALAYI_HIGH_DOSE_DN |
0.0035714 |
0.0197796 |
-0.5595859 |
-2.907197 |
0 |
184 |
down |
| QI_PLASMACYTOMA_UP |
0.0036496 |
0.0197796 |
-0.5389177 |
-2.905090 |
0 |
243 |
down |
| GSE10325_LUPUS_BCELL_VS_LUPUS_MYELOID_DN |
0.0035587 |
0.0197796 |
-0.5549483 |
-2.901693 |
0 |
192 |
down |
| TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_HSC_DN |
0.0035088 |
0.0197796 |
-0.5585107 |
-2.891660 |
0 |
177 |
down |
| GSE22140_HEALTHY_VS_ARTHRITIC_GERMFREE_MOUSE_CD4_TCELL_DN |
0.0035842 |
0.0197796 |
-0.5534128 |
-2.887153 |
0 |
191 |
down |
| GSE10325_BCELL_VS_MYELOID_DN |
0.0035587 |
0.0197796 |
-0.5549508 |
-2.885526 |
0 |
183 |
down |
| GSE7218_UNSTIM_VS_ANTIGEN_STIM_THROUGH_IGG_BCELL_DN |
0.0034364 |
0.0197796 |
-0.5660759 |
-2.884559 |
0 |
159 |
down |
| GSE9006_HEALTHY_VS_TYPE_2_DIABETES_PBMC_AT_DX_UP |
0.0035842 |
0.0197796 |
-0.5568072 |
-2.883340 |
0 |
181 |
down |
| GSE23568_CTRL_TRANSDUCED_VS_WT_CD8_TCELL_DN |
0.0034843 |
0.0197796 |
-0.5521093 |
-2.880758 |
0 |
188 |
down |
| GSE24634_TREG_VS_TCONV_POST_DAY10_IL4_CONVERSION_DN |
0.0034843 |
0.0197796 |
-0.5485671 |
-2.862276 |
0 |
188 |
down |
| BASSO_CD40_SIGNALING_UP |
0.0029674 |
0.0197796 |
-0.6003008 |
-2.857327 |
0 |
100 |
down |
| NIKOLSKY_BREAST_CANCER_16P13_AMPLICON |
0.0030675 |
0.0197796 |
-0.5964448 |
-2.839071 |
0 |
105 |
down |